Update docker images to reduce security vulnerabilities

[adthrasher]

This resolves 960 security vulnerabilities. Mainly by switching compatible images to an alpine base image. Other improvements include updating base OS versions and updating packages. There are 25 remaining security vulnerabilities, all of which are Low/Medium by Snyk (level documentation). All of the remaining vulnerabilities are in the util image (which uses Ubuntu 24.04). We do an apt-get upgrade in the image and I've skimmed most of the remaining vulnerabilities and they have no fixed version in 24.04. So the only "fix" would be to change to a different image that does not have those vulnerabilities.

One important thing to note, the Python alpine-based images (python:3.13.1-alpine) are all using the 3.21 release from 12/05/2024. So it's unlikely that it has no vulnerabilities, but rather that those have not been discovered and reported. Here is the list from the prior 3.20 release. The R image (ghcr.io/r-hub/r-minimal/r-minimal:4.4.2) uses the older 3.19 release with slightly more vulnerabilities.

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• The code passes all CI tests without any errors or warnings.
• You have added tests (when appropriate).
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• If you have made any changes to the scripts/ or docker/ directories, please ensure any image versions have been incremented accordingly!
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[github-advanced-security]

Snyk Container found more than 20 potential problems in the proposed changes. Check the Files changed tab for more details.

[adthrasher]

Tagging @mcrusch and @claymcleod so they're aware. Specifically, since Mike and I discussed security vulnerabilities last week.

[adthrasher]

Also tagging @kevin-benton as his team has significantly more experience with security vulnerability scanning.

[claymcleod]

Seems reasonable to me.

[a-frantz]

Approving even though when you switch the container values back to main my review will be dismissed